Statistical Applications in Genetics and Molecular Biology

2002 - 2009

from Berkeley Electronic Press
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Volume 8, issue 1, 2009

Inferring Dynamic Genetic Networks with Low Order Independencies

Sophie Lèbre

Hypothesis Tests for Point-Mass Mixture Data with Application to `Omics Data with Many Zero Values

Sandra Taylor and Katherine Pollard

A Multiple Testing Approach to High-Dimensional Association Studies with an Application to the Detection of Associations between Risk Factors of Heart Disease and Genetic Polymorphisms

José A. Ferreira, Johannes Berkhof, Olga Souverein and Koos Zwinderman

Composite Likelihood Modeling of Neighboring Site Correlations of DNA Sequence Substitution Rates

Ling Deng and Dirk F. Moore

A Nonlinear Mixed-Effects Model for Estimating Calibration Intervals for Unknown Concentrations in Two-Color Microarray Data with Spike-Ins

Pushpike J. Thilakarathne, Geert Verbeke, Kristof Engelen and Kathleen Marchal

A Unified Mixed Effects Model for Gene Set Analysis of Time Course Microarray Experiments

Lily Wang, Xi Chen, Russell D. Wolfinger, Jeffrey L. Franklin, Robert J. Coffey and Bing Zhang

Statistical Screening Method for Genetic Factors Influencing Susceptibility to Common Diseases in a Two-Stage Genome-Wide Association Study

Yasunori Sato, Nan Laird, Hideki Suganami, Chikuma Hamada, Naoto Niki, Isao Yoshimura and Teruhiko Yoshida

A Regularized Regression Approach for Dissecting Genetic Conflicts that Increase Disease Risk in Pregnancy

Shaoyu Li, Qing Lu, Wenjiang Fu, Roberto Romero and Yuehua Cui

Transmission Disequilibrium Test Power and Sample Size in the Presence of Locus Heterogeneity

Chuanwen Chen, Guang Yang, Steven Buyske, Tara Matise, Stephen J. Finch and Derek Gordon

Characterizing the D2 Statistic: Word Matches in Biological Sequences

Sylvain Forêt, Susan R. Wilson and Conrad J. Burden

MC-Normalization: A Novel Method for Dye-Normalization of Two-Channel Microarray Data

Mattias Landfors, Jessica Fahlén and Patrik Rydén

M-quantile Regression Analysis of Temporal Gene Expression Data

Veronica Vinciotti and Keming Yu

Modeling Dependence in Methylation Patterns with Application to Ovarian Carcinomas

Michelle R. Lacey and Melanie Ehrlich

Dimension Reduction of Microarray Data in the Presence of a Censored Survival Response: A Simulation Study

Tuan S. Nguyen and Javier Rojo

Calculating Asymptotic Significance Levels of the Constrained Likelihood Ratio Test with Application to Multivariate Genetic Linkage Analysis

Nathan J. Morris, Robert Elston and Catherine M. Stein

A Statistical Model for Genetic Mapping of Viral Infection by Integrating Epidemiological Behavior

Yao Li, Arthur Berg, Myron N. Chang, Ping Du, Kwangmi Ahn, David Mauger, Duanping Liao and Rongling Wu

Identifying Individuals in a Complex Mixture of DNA with Unknown Ancestry

Joshua Sampson and Hongyu Zhao

Prediction of Motifs Based on a Repeated-Measures Model for Integrating Cross-Species Sequence and Expression Data

Elizabeth A. Siewert and Katerina J. Kechris

Ancestral Recombination Graphs under Non-Random Ascertainment, with Applications to Gene Mapping

Ola Hössjer, Linda Hartman and Keith Humphreys

Rotation Testing in Gene Set Enrichment Analysis for Small Direct Comparison Experiments

Guro Dørum, Lars Snipen, Margrete Solheim and Solve Sæbø

A Multivariate Growth Curve Model for Ranking Genes in Replicated Time Course Microarray Data

Jemila S. Hamid and Joseph Beyene

Estimation of Selection Intensity under Overdominance by Bayesian Methods

Erkan Ozge Buzbas, Paul Joyce and Zaid Abdo

Model Selection Based on FDR-Thresholding Optimizing the Area under the ROC-Curve

Alexandra C. Graf and Peter Bauer

Adaptive Transmission Disequilibrium Test for Family Trio Design

Min Yuan, Xin Tian, Gang Zheng and Yaning Yang

Sequential Analysis for Microarray Data Based on Sensitivity and Meta-Analysis

Guillemette Marot and Claus-Dieter Mayer

A Non-Homogeneous Hidden-State Model on First Order Differences for Automatic Detection of Nucleosome Positions

Pei Fen Kuan, Dana Huebert, Audrey Gasch and Sunduz Keles

Extensions of Sparse Canonical Correlation Analysis with Applications to Genomic Data

Daniela M. Witten and Robert J. Tibshirani

Bayesian Unsupervised Learning with Multiple Data Types

Phaedra Agius, Yiming Ying and Colin Campbell

A Parametric Model for Analyzing Anticipation in Genetically Predisposed Families

Klaus Larsen, Janne Petersen, Inge Bernstein and Mef Nilbert

Increase of Rejection Rate in Case-Control Studies with the Differential Genotyping Error Rates

Kwangmi Ahn, Derek Gordon and Stephen J. Finch

Incorporating Duplicate Genotype Data into Linear Trend Tests of Genetic Association: Methods and Cost-Effectiveness

Bryce Borchers, Marshall Brown, Brian McLellan, Airat Bekmetjev and Nathan L. Tintle

Weighted Multiple Hypothesis Testing Procedures

Guolian Kang, Keying Ye, Nianjun Liu, David B. Allison and Guimin Gao

Multilevel Comparison of Dendrograms: A New Method with an Application for Genetic Classifications

János Podani, Attila Engloner and Agnes Major

Univariate Shrinkage in the Cox Model for High Dimensional Data

Robert J. Tibshirani

Balanced Gradient Boosting from Imbalanced Data for Clinical Outcome Prediction

Reiji Teramoto

Orthology-Based Multilevel Modeling of Differentially Expressed Mouse and Human Gene Pairs

Benjamin A. Ogorek and Leonard A. Stefanski

Testing of Chromosomal Clumping of Gene Properties

Luciano Fernandez-Ricaud, Daniel Dalevi, Anders Blomberg and Olle Nerman

A Multilocus Model for Constructing a Linkage Disequilibrium Map in Human Populations

Qin Li and Rongling Wu

Impact of Population Stratification on Family-Based Association Tests with Longitudinal Measurements

Xiao Ding, Scott Weiss, Benjamin Raby, Christoph Lange and Nan M. Laird

Score Statistics for Mapping Quantitative Trait Loci

Myron N. Chang, Rongling Wu, Samuel S. Wu and George Casella

Two-Stage Model-Based Clustering for Liquid Chromatography Mass Spectrometry Data Analysis

Marta Łuksza, Bogusław Kluge, Jerzy Ostrowski, Jakub Karczmarski and Anna Gambin

Survival Analysis with High-Dimensional Covariates: An Application in Microarray Studies

David Engler and Yi Li

Detecting Outlier Samples in Microarray Data

Albert D. Shieh and Yeung Sam Hung

Modified FDR Controlling Procedure for Multi-Stage Analyses

Catherine Tuglus and Mark J. van der Laan

A Bayesian Analysis Strategy for Cross-Study Translation of Gene Expression Biomarkers

Joseph Lucas, Carlos Carvalho and Mike West

Normalization Method for Transcriptional Studies of Heterogeneous Samples – Simultaneous Array Normalization and Identification of Equivalent Expression

Li-Xuan Qin and Jaya M. Satagopan

Sparse Canonical Correlation Analysis with Application to Genomic Data Integration

Elena Parkhomenko, David Tritchler and Joseph Beyene

Volume 7, issue 2, 2008

Empirical Bayes Logistic Regression

Foteini Strimenopoulou and Philip J. Brown

A Classification Model for the Leiden Proteomics Competition

Huub C. J. Hoefsloot, Suzanne Smit and Age K. Smilde

Classification of Breast Cancer versus Normal Samples from Mass Spectrometry Profiles Using Linear Discriminant Analysis of Important Features Selected by Random Forest

Somnath Datta

Principal Component Discriminant Analysis

Tom Fearn

Developing a Discrimination Rule between Breast Cancer Patients and Controls Using Proteomics Mass Spectrometric Data: A Three-Step Approach

A. Geert Heidema and Nico Nagelkerke

Application of the Random Forest Classification Method to Peaks Detected from Mass Spectrometric Proteomic Profiles of Cancer Patients and Controls

Jennifer H. Barrett and David A. Cairns

Organizing a Competition on Clinical Mass Spectrometry Based Proteomic Diagnosis

Bart Mertens

Case-Control Breast Cancer Study of MALDI-TOF Proteomic Mass Spectrometry Data on Serum Samples

Martijn P. J. van der Werff, Bart Mertens, Mirre E. de Noo, Marco R. Bladergroen, Hans C. Dalebout, Rob A. E. M. Tollenaar and Andre M. Deelder

Breast Cancer Diagnosis from Proteomic Mass Spectrometry Data: A Comparative Evaluation

David J. Hand

Assessing the Validity Domains of Graphical Gaussian Models in Order to Infer Relationships among Components of Complex Biological Systems

Fanny Villers, Brigitte Schaeffer, Caroline Bertin and Sylvie Huet

Clinical Mass Spectrometry Proteomic Diagnosis by Conformal Predictors

Alex Gammerman, Ilia Nouretdinov, Brian Burford, Alexey Chervonenkis, Vladimir Vovk and Zhiyuan Luo

A Cross-Validation Study to Select a Classification Procedure for Clinical Diagnosis Based on Proteomic Mass Spectrometry

Dirk Valkenborg, Suzy Van Sanden, Dan Lin, Adetayo Kasim, Qi Zhu, Philippe Haldermans, Ivy Jansen, Ziv Shkedy and Tomasz Burzykowski

Support Vector Machine Approach to Separate Control and Breast Cancer Serum Samples

Thang V. Pham, Mark A. van de Wiel and Connie R. Jimenez

Autocorrelated Logistic Ridge Regression for Prediction Based on Proteomics Spectra

Jelle J. Goeman

International Competition on Mass Spectrometry Proteomic Diagnosis

Bart Mertens

Volume 7, issue 1, 2008

Structure Learning in Nested Effects Models

Achim Tresch and Florian Markowetz

Calculating Confidence Intervals for Prediction Error in Microarray Classification Using Resampling

Wenyu Jiang, Sudhir Varma and Richard Simon

Comparing the Characteristics of Gene Expression Profiles Derived by Univariate and Multivariate Classification Methods

Manuela Zucknick, Sylvia Richardson and Euan A. Stronach

Drifting Markov Models with Polynomial Drift and Applications to DNA Sequences

Nicolas Vergne

Accommodating Uncertainty in a Tree Set for Function Estimation

Brian C. Healy, Victor G. DeGruttola and Chengcheng Hu

Nonparametric Functional Mapping of Quantitative Trait Loci Underlying Programmed Cell Death

Yuehua Cui, Rongling Wu, George Casella and Jun Zhu

A Sparse PLS for Variable Selection when Integrating Omics Data

Kim-Anh Lê Cao, Debra Rossouw, Christèle Robert-Granié and Philippe Besse

Addressing the Shortcomings of Three Recent Bayesian Methods for Detecting Interspecific Recombination in DNA Sequence Alignments

Dirk Husmeier and Alexander V. Mantzaris

Supervised Distance Matrices

Katherine S. Pollard and Mark J. van der Laan

Importance Sampling for the Infinite Sites Model

Asger Hobolth, Marcy K. Uyenoyama and Carsten Wiuf

A Unification of Multivariate Methods for Meta-Analysis of Genetic Association Studies

Pantelis G. Bagos

Pattern Classification of Phylogeny Signals

Xiaofei Shi, Hong Gu and Chris Field

Quantifying the Association between Gene Expressions and DNA-Markers by Penalized Canonical Correlation Analysis

Sandra Waaijenborg, Philip C. Verselewel de Witt Hamer and Aeilko H. Zwinderman

Reducing Spatial Flaws in Oligonucleotide Arrays by Using Neighborhood Information

Jose Manuel Arteaga-Salas, Andrew P. Harrison and Graham J. G. Upton

Statistical Methods in Integrative Analysis for Gene Regulatory Modules

Lingmin Zeng, Jing Wu and Jun Xie

A Composite-Conditional-Likelihood Approach for Gene Mapping Based on Linkage Disequilibrium in Windows of Marker Loci

Fabrice Larribe and Sabin Lessard

Approximately Sufficient Statistics and Bayesian Computation

Paul Joyce and Paul Marjoram

Data Distribution of Short Oligonucleotide Expression Arrays and Its Application to the Construction of a Generalized Intellectual Framework

Tomokazu Konishi

Estimating Number of Clusters Based on a General Similarity Matrix with Application to Microarray Data

Shafagh Fallah, David Tritchler and Joseph Beyene

Collapsing SNP Genotypes in Case-Control Genome-Wide Association Studies Increases the Type I Error Rate and Power

Abigail G. Matthews, Chad Haynes, Chang Liu and Jurg Ott

A Comparison of Normalization Techniques for MicroRNA Microarray Data

Youlan Rao, Yoonkyung Lee, David Jarjoura, Amy S. Ruppert, Chang-gong Liu, Jason C. Hsu and John P. Hagan

Predicting Protein Concentrations with ELISA Microarray Assays, Monotonic Splines and Monte Carlo Simulation

Don Simone Daly, Kevin K. Anderson, Amanda M. White, Rachel M. Gonzalez, Susan M. Varnum and Richard C. Zangar

The Estimator of the Optimal Measure of Allelic Association: Mean, Variance and Probability Distribution When the Sample Size Tends to Infinity

Brigitte Mangin, Pauline Garnier-Géré and Christine Cierco-Ayrolles

Coalescent Time Distributions in Trees of Arbitrary Size

Sam Efromovich and Laura Salter Kubatko

Phenotyping Genetic Diseases Using an Extension of µ-Scores for Multivariate Data

José F. Morales, Tingting Song, Arleen D. Auerbach and Knut M. Wittkowski

Modeling DNA Methylation in a Population of Cancer Cells

Kimberly D. Siegmund, Paul Marjoram and Darryl Shibata

Detecting Two-Locus Gene-Gene Effects Using Monotonisation of the Penetrance Matrix

Susanne Henningsson and Staffan I. Nilsson

A SNP Streak Model for the Identification of Genetic Regions Identical-by-descent

Gregory Leibon, Daniel N. Rockmore and Martin R. Pollak

Semi-Parametric Differential Expression Analysis via Partial Mixture Estimation

David Rossell, Rudy Guerra and Clayton Scott

Re-Cracking the Nucleosome Positioning Code

Mark R. Segal

Adaptive Choice of the Number of Bootstrap Samples in Large Scale Multiple Testing

Wenge Guo and Shyamal Peddada

Adapting Prediction Error Estimates for Biased Complexity Selection in High-Dimensional Bootstrap Samples

Harald Binder and Martin Schumacher

TRAB: Testing Whether Mutation Frequencies Are Above an Unknown Background

Giovanni Parmigiani, Sining Chen and Victor E. Velculescu

Correcting the Estimated Level of Differential Expression for Gene Selection Bias: Application to a Microarray Study

David R. Bickel

Self-Organizing Maps with Statistical Phase Synchronization (SOMPS) for Analyzing Cell Cycle-Specific Gene Expression Data

Chang Sik Kim